Gene expression profile analysis of residual feed intake for Isfahan native chickens using RNA-SEQ data

摘要

The factors that affect residual feed intake (RFI) of two chicken breeds (Ross as commercial andIsfahan as Iranian local breed with low and high RFI, respectively) were examined. Wesequenced their liver transcriptomes using RNA-Seq while focusing on the identification ofimportant candidate genes, which might influence RFI and growth rate. The differential geneexpression analysis revealed that 121 and 279 known genes were significantly up- and downregulated in the local breed, respectively. QTL enrichment analysis revealed that 63 down-regulated genes in the local breed were enriched in the QTL regions related to feed efficiency traits.Moreover, the functional enrichment analysis showed that the down-regulated genes in thenative chickens were mainly involved in the different metabolic processes, such as carboxylicacid metabolic process and response to stress. The Differentially Expressed Genes exploredbetween the chickens of the two breeds led to the identification of some important candidategenes for further breed improvement programmes, including RSAD2, IL15, LIPI, EGR1 andDUSP16. These findings will be a useful resource for the biological investigations of RFI-relatedgenes in Isfahan local chickens and may provide some clues for understanding the moleculargenetic mechanisms in other chicken breeds.